Mass holding centres that Germany’s interior ministry wants to roll out across the country will stoke social tension between locals and migrants and undermine the welcoming image the country has gained in the eyes of the world, aid organisations have said.

So-called anchor centres – an acronym for arrival, decision, return – are designed to speed up deportations of unsuccessful asylum seekers, by containing large groups of people and the authorities who rule on their claims inside the same holding facility.

Until now, Germany’s policy has been to embed new arrivals in communities across the country. But Angela Merkel’s government is seeking to reverse its strategy, as a populist backlash builds against the chancellor’s handling of the refugee crisis.

“We all know how difficult it is to deport people without protected status after they have been spread out across the country and put down roots in our cities and communities,” the interior minister, Horst Seehofer, told the German parliament last week.

“In the future the end of an asylum application will coincide with the start of the deportation procedure,” said the leader of the CSU and former Bavarian state premier, adding that he wanted to see states set up the new centres this autumn.

But the transit centre in Seehofer’s home state that is meant to work as a prototype for the scheme has experienced high crime rates, mass protests and rising tensions between asylum seekers and security forces, the Guardian found during a visit to the Max-Immelmann barracks in Manching.

The converted army compound is part of a complex outside Ingolstadt, Upper Bavaria, that holds about 1,100 people, mainly from the west Balkans, Ukraine, Nigeria and Afghanistan.

“It is like a prison,” said Lucky Raphael, 24, from Nigeria, who said inmates were not allowed to lock their rooms, cook their own food, or go outside to seek work or attend school. “We can go outside, but always in the fear that we could be arrested,” said Raphael, who said he left his home country because of his dire economic and social circumstances, and arrived in Bavaria via Italy.

Raphael said had been living in the Manching transit centre for 11 months, though authorities say the average length of stay for people who have arrived here since September 2015 is four-and-a-half months.

Bavarian authorities hope to speed up the checking process with technology. They analyse metadata on smartphones and run speech samples through a “voice geometry” programme to determine the travel route and ethnic background of applicants who do not have passports.

They are reacting to an increasingly heated political debate about Germany’s failure to deport asylum seekers whose applications have been rejected. Anis Amri, a Tunisian who in December 2016 killed 12 people by driving a truck into a crowd at a Berlin Christmas market, had been rejected but not deported. In 2017, about half a million unsuccessful asylum seekers remained in the country.

Anchor centres “send out a signal to people who have low chances of being allowed to stay,” said Daniel Waidelich of the Upper Bavarian government. “It’s not worth coming to Germany, because your claim is processed very quickly here.” Since September 2015, the centre in Manching has carried out 1,000 deportations, while 2,500 inmates have left voluntarily.

Critics say the new centres create an absurd double-bind on those inmates at the transit centres who have realistic chances of being granted asylum: while they are actively hindered from integrating into German society while their application is pending, they are expected to immediately integrate as soon as they get the all-clear.

Of asylum applications from Nigeria in Upper Bavaria, 17% have succeeded in gaining the applicants protected status, many of them women who have been forced into prostitution, others Christian minorities persecuted by Boko Haram in the country’s north-east.

“Integration is like a four-legged table,” said Willi Dräxler of the Catholic aid charity Caritas, which has four people doing regular voluntary work at Manching. “Language, contacts in the local community, a job and a home are all vital ingredients. If you saw off one leg, the table is going to wobble. Within these transit centres, however, integration isn’t happening at all.”

A former army base in Manching, used a a transit centre for asylum seekers Photograph: Philip Oltermann for the Guardian

Inside the centres, frustration with long waits often boils over. “We are not told why we are here,” said Kelvi Batin, also from Nigeria. “It would be better if they told us straight away when we arrived that we cannot stay”.

While Manching has not seen incidents like the one at a centre in Ellwangen, Baden–Württemberg, where 200 asylum seekers tried prevent the deportation of one inmate, police have to intervene at the compound on a daily basis. In 2017 the police were called 355 times to the Manching transit centre complex.

During a recent media tour of the premises, a group of Nigerians staged an impromptu protest, chanting “We want our freedom” and holding up handmade signs reading: “We’re tired of living in camps. Please, we need transfer.”

Dräxler said: “Protests about seemingly small issues like food are often actually protests about the conditions in these centres as a whole. The main source of troubles is that the people inside have no perspective and aren’t allowed to work.”

The inability of the migrants inside the centre to engage themselves in the community was also stoking resentment and prejudice among the local population, said Gabriele Störkle of the Caritas centre in Pfaffenhofen. “These transit centres are like black boxes; the local population isn’t allowed to go inside, so they project all their greatest fear into what is going on inside them.”

“Three years ago, Germany was globally admired for its welcoming culture – the pictures from train stations in Munich travelled around the world,” said Dräxler. “What has happened to that culture? Now there is only fear of refugees.”